Hopper minecarts will not pick up entities through blocks. I do not know if this was patched in 15w41b.

Steps
Hopper minecart running under dirt.
villager harvests wheat and the entity sits on top of dirt with new seeds planted
hopper runs under dirt and doesnt pick up entity through dirt block.

Also tested it without the dirt or anything there. the hopper minecart wouldnt pick up any entities on the ground at all